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Two undergraduates working on research projects in MCB laboratoriesKatie Rose Clapham, 2008 (Losick lab) and Elisa Zhang, 2008 (Maniatis lab)were recently awarded Hoopes Prizes for their senior theses. According to the FAS Prizes website, the Hoopes Prize for Excellence in the Work of Undergraduates was established in 1982 from the estate of Thomas Temple Hoopes, 1919, to “grant awards to undergraduates on the basis of outstanding scholarly work or research.” Katie Rose and Elisa were among 83 undergraduates awarded the prestigious prize, and each will receive a cash award of $3,500.

Elisa Zhang Examines Principles of Gene Regulation by miRNAs

(L-R) Eugene Makeyev, Elisa Zhang, and Tom Maniatis

Elisa Zhang’s research, carried out under the supervision of Dr. Eugene Makeyev, a post-doctoral fellow in the Maniatis lab, involved examining the targets of a microRNA called miR-124. miRNAs are small noncoding RNAs that regulate gene expression by suppressing translation and/or destabilizing mRNAs bearing complementary target sequences within their 3′ untranslated regions.

“We have recently shown that a microRNA called miR-124 is expressed at low levels in neural progenitor cells and at high levels in developing and mature neurons,” says Tom Maniatis. “This graded expression suggested the possibility that distinct subsets of miRNA targets are downregulated in the corresponding cell types.” (

Elisa’s project involved generating a library of luciferase reporter constructs containing the 3’UTRs of natural miR-124 targets. She then established a neuronal cell culture assay to examine the activity of the reporter in the presence of varying levels of miR-124.

“Remarkably, targets that are sensitive to low miRNA concentration do not necessarily show a more complete inhibition at high miRNA concentrations and vice versa,” says Maniatis. “This finding indicates that the molecular principles underlying the miRNA regulation are more complex than appreciated previously, and suggest an interesting line of future research.”

Of her performance in the lab, both Makeyev and Maniatis praised Elisa’s dedication and enthusiasm, and the pride she took in getting experiments to work. “It was a pleasure to work with Elisa. She is a very smart and motivated student who doesn’t give up when an experiment doesn’t work the first time,” says Makeyev. Maniatis goes on to say, “She has been essentially independent in both planning and carrying out her experiments to an extent that is unusual for an undergraduate student. Elisa ranks among the top undergraduates to have worked in my lab, and her thesis is exceptional.”

“Working in the Maniatis lab was the most defining academic experience of my time at Harvard,” says Elisa. “Eugene [Makeyev] and Professor Maniatis were exceptional mentors. In my day-to-day work, Eugene always took an active interest in my scientific progress, and my interactions with Professor Maniatis really helped me gain a deeper appreciation for the scientific vision for the project. The lab as a whole has been extraordinarily supportiveI’ve learned so much from everyone I interacted with in my time in the lab.”

In addition to a Hoopes Prize, Elisa is a Fulbright recipient, and will spend the next year at the EMBL in Heidelberg, Germany, working in Andreas Ladurner’s lab studying chromatin dynamics. After that, she will pursue a PhD in the Department of Molecular and Cell Biology at UC Berkeley.

Elisa’s thesis is entitled Distinct Sets of mRNA Targets Exhibit Differential miRNA Dose Response.


Katie Rose Clapham Elucidates the Function of a Small Protein in Bacillus Sporulation

(L-R) Kumaran Ramamurthi, Katie Rose Clapham, and Rich Losick

In addition to receiving a Hoopes Prize for her thesis entitled A Tiny Protein Links Two Morphogenetic Processes in a Bacterium, Katie Rose Clapham was the recipient of two additional awards: the Lawrence J. Henderson Prize, awarded annually to the student submitting the very best thesis in Biochemical Sciences, and the Raymond W. Sarber Award of the American Society for Microbiology, which recognizes the best undergraduate research in the field of microbiology. As the Henderson Prize winner, Katie Rose will receive a $350 book award, a framed certificate, and a copy of the book Fitness of the Environment by Lawrence Henderson.

Katie Rose’s project concerns a tiny, 26 amino acid protein called SpoVM that plays a pivotal role in morphogenesis in the spore-forming bacterium Bacillus subtilis. SpoVM sits in a membrane that surrounds the developing spore, where it recruits proteins that form a protein shell known as the “coat” around the membrane. This, in turn, triggers the production of a thick layer of cell wall material known as the cortex.

According to Richard Losick, “SpoVM poses three key questions: How does it sit in the membrane? How does it recruit coat proteins? And, most mysteriously, how does it trigger cortex synthesis?”

SpoVM forms a helical structure with hydrophobic amino acids on one face and hydrophilic residues on the other. Working with Dr. Kumaran Ramamurthi, Katie Rose elucidated both how SpoVM sits in the membrane and how it triggers cortex synthesis. “Katie Rose built amino acid substitution mutants of residues on both faces of the helix, and together with Ramamurthi showed that it is the hydrophobic face of the helix that inserts parallel to and into the membrane, thereby overturning a model in the literature that said the opposite,” explains Losick.

To address the more challenging question as to how SpoVM triggers cortex synthesis, Katie Rose performed a genetic screen. Using one of her amino acid substitution mutants that was defective in cortex synthesis, she identified and mapped extragenic suppressor mutations that restore spore formation to her mutant.

“She hit pay dirt with the isolation of a suppressor that exhibits a property called allele-specificity, which suggests that it identifies a gene that might be a downstream target of SpoVM,” says Losick. Katie Rose then mapped the suppressor mutation to a small region of the chromosome that contains two previously known genes and several previously uncharacterized genes, and showed that it is not one of the known genes. She is close to pinpointing which of the unknown genes is the site of her suppressor mutation.

“This is exciting,” continues Losick, “because she is on the verge of elucidating an important step in a previously mysterious pathway of morphogenesis and assigning a function to a previously uncharacterized gene. This work is likely to culminate in a publication on which Katie Rose will be an author and will, I anticipate, spark much interest in the sporulation field.”

Katie Rose expressed enthusiasm about her time in the Losick lab. “It was an honor to have the opportunity to work with Kumaran [Ramamurthi] and Professor LosickI was very lucky to have such exceptional mentors,” she says. “My research experience taught me what kind of scientific questions one can ask and how to address those questions experimentally in a way that cannot be conveyed in a classroom.”

In addition to her work in the Losick lab, Katie Rose spent six months in Rosario, Argentina, working in the laboratory of Professor Diego de Mendoza, an HHMI International Scholar. In the de Mendoza lab, she worked on the control of fatty acid metabolism genes in Bacillus subtilis during vegetative growth and sporulation, and included that work in her thesis.

“My time in Argentina was a time of great personal growth,” says Katie Rose. “It gave me an opportunity to be independent, make friends in another language, and learn about another culture.”

Regarding her scientific experience, Katie Rose appreciated the opportunity to experience firsthand how science is performed in another country. “Though I was working on spore formation in Bacillus, the protocols and procedures differed somewhat from those used in the Losick lab, and this gave me the opportunity to think more carefully and creatively about my experiments.”

“Working with Katie Rose was a lot of fun,” says Ramamurthi. “She’s bright and creative, but what really set her apart is that she showed up to our lab as a freshmannot as part of a class requirement for course credit, but on her ownand displayed a genuine curiosity and interest in basic science. When a student has an outlook like that, mentoring is a piece of cake!”

“Briefly put, I rank Katie Rose’s thesis among the top two or three of the many senior theses from my lab over the past 35 years,” says Losick. “She carried out sophisticated experiments independently, and did an outstanding job of writing up her four years of research in a lucid and well-reasoned manner.”

Katie Rose plans to attend medical school in the fall.